Need some help here...
I brewed my version of a Chocolate Stout and added 1/4 cup of cocoa powder for the last 3 minutes of the boil and another 1/4 cup when I transferred it to the secondary fermenter. I didn't notice a real chocolate taste when I transferred it to the secondary, so I was planning to add a vial (or two) of the Home Brewers Chocolate flavoring when I keg it. Any suggestions?

My best suggestion is to stop trying to fix a beer that is not as good as you like. You have already added a ton of chocolate. Is it sweetness that you lack? If you simply lack chocolate flavor perhaps you could increase the chocolate malt. Ideally I avoid post fermentation additions unless the flavor can not be created with malt, yeast, and hops.

I like Crisp chocolate for a pure chocolate taste and MFB chocolate for a more complex raisin and dark chocolate flavor.

This looks pretty darn good for a recipe. I would actually expect a healthy amount of chocolate flavor in 8 oz of chocolate malt. If you do add chocolate to the finished beer try it first on a glass or two and when you have found the appropriate amount do the whole batch.

I can see why you didn't get much chocolate flavor from only 1/4 cup of cocoa powder. I use 8oz by weight of cocoa powder in the last 10 minutes of the boil for 5 gallons. I get a nice chocolate flavor from that single chocolate addition along with the use of some chocolate malt in the mash. 1/4 cup of cocoa powder weighs only about an ounce so that's way under what you would need. Next time you brew this beer just increase the cocoa powder and see if you get what you want from that. Also some have used cocoa nibs in secondary with success.